[Bioperl-l] Bio::Tools::Run::WrapperBase: Capture the command thatis executed?

Peter biopython at maubp.freeserve.co.uk
Mon Apr 19 10:09:03 EDT 2010

On Mon, Apr 19, 2010 at 2:03 PM, Mark A. Jensen <maj at fortinbras.us> wrote:
> Hey Ben,
> Yes, the new stuff is in the bioperl-dev/trunk
> svn://code.open-bio.org/bioperl/bioperl-dev/trunk/Bio/Tools/Run
> (code.open-bio.org was working as of this morning...)
> This is all pretty experimental, so use at own risk. The XML-based
> config system is experimental too at the moment (tho' all code
> is available, in bioperl-dev/trunk/Bio/Tools). I've been getting
> good feedback from other Bio* peeps, who are advocating using an
> existing config standard like emboss ACD or the Galaxy format.

The EMBOSS ACD format is text based and as such rather niche.
I was more suggesting the ability to parse the EMBOSS ACD files
into the chosen XML format would be a neat way to automatically
generate wrappers for all the EMBOSS tools at once.

The Galaxy workflow command line tool description is XML and,
might be suitably general. There are likely others out there too
(no sense reinventing the wheel if possible).

> I'll likely convert the wrappermaker system to using one of those,
> but the custom format (in maker.xsd in bioperl-dev) will be there to
> experiment with.
> (To the list, any comments regarding this issue are welcome, see
> http://bioperl.org/wiki/HOWTO:Wrappers for an overview of
> this project)
> cheers MAJ



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